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The Neolithic Transition in the Baltic Was Not Driven

by Admixture with Early European Farmers

Highlights

d

A degree of genetic continuity from the Mesolithic to the

Neolithic in the Baltic

d

Steppe-related genetic influences found in the Baltic during

the Neolithic

d

No Anatolian farmer-related genetic admixture in Neolithic

Baltic samples

d

Steppe ancestry in Latvia at the time of the emergence of

Balto-Slavic languages

Authors

Eppie R. Jones, Gunita Zarina,

Vyacheslav Moiseyev, ...,

Andrea Manica, Ron Pinhasi,

Daniel G. Bradley

Correspondence

erj35@cam.ac.uk (E.R.J.),

am315@cam.ac.uk (A.M.),

ron.pinhasi@ucd.ie (R.P.),

dbradley@tcd.ie (D.G.B.)

In Brief

Jones et al. present genome-wide data

spanning the Mesolithic-Neolithic

transition in Latvia and Ukraine that show

that massive migration of Anatolian

farmers was not a universal driver for the

spread of Neolithic lifeways and possibly

Indo-European languages throughout

Europe.

Jones et al., 2017, Current Biology27, 576–582

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Current Biology

Report

The Neolithic Transition in the Baltic Was Not

Driven by Admixture with Early European Farmers

Eppie R. Jones,1,2,*Gunita Zarina,3Vyacheslav Moiseyev,4Emma Lightfoot,5Philip R. Nigst,6Andrea Manica,2,* Ron Pinhasi,7,*and Daniel G. Bradley1,8,*

1Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland

2Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK 3Institute of Latvian History, University of Latvia, Kalpaka Bulvaris 4, Rıga 1050, Latvia

4Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia 5McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK

6Division of Archaeology, Department of Archaeology and Anthropology, University of Cambridge, Downing Street, Cambridge CB2 3DZ, UK 7School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland

8Lead Contact

*Correspondence:erj35@cam.ac.uk(E.R.J.),am315@cam.ac.uk(A.M.),ron.pinhasi@ucd.ie(R.P.),dbradley@tcd.ie(D.G.B.)

http://dx.doi.org/10.1016/j.cub.2016.12.060

SUMMARY

The Neolithic transition was a dynamic time in

Euro-pean prehistory of cultural, social, and technological

change. Although this period has been well explored

in central Europe using ancient nuclear DNA [

1, 2

], its

genetic impact on northern and eastern parts of this

continent has not been as extensively studied. To

broaden our understanding of the Neolithic

transi-tion across Europe, we analyzed eight ancient

ge-nomes: six samples (four to

1- to 4-fold coverage)

from a 3,500 year temporal transect (

8,300–4,800

calibrated years before present) through the Baltic

region dating from the Mesolithic to the Late

Neolithic and two samples spanning the

Meso-lithic-Neolithic boundary from the Dnieper Rapids

region of Ukraine. We find evidence that some

hunt-er-gatherer ancestry persisted across the Neolithic

transition in both regions. However, we also find

sig-nals consistent with influxes of non-local people,

most likely from northern Eurasia and the Pontic

Steppe. During the Late Neolithic, this

Steppe-related impact coincides with the proposed

emer-gence of Indo-European languages in the Baltic

region [

3, 4

]. These influences are distinct from the

early farmer admixture that transformed the genetic

landscape

of

central

Europe,

suggesting

that

changes associated with the Neolithic package in

the Baltic were not driven by the same

Anatolian-sourced genetic exchange.

RESULTS

Sample Context and Genomic Data

In Europe, the Neolithic transition marked the beginning of a period of innovations that saw communities shift from a mobile lifestyle, dependent on hunting and gathering for survival, to a

more sedentary way of life based on food production. This new lifeway, which originated in the Near East 11,500 calibrated years before present (cal BP) [5, 6], had arrived in southeast Eu-rope by8,500 cal BP [7], from where it spread quickly across the continental interior of Europe and introduced animal hus-bandry, cultivated cereals, pottery, and ground stone tools to the region. There is a long-standing debate among archaeolo-gists whether this spread was due to the dispersal of farmers into new lands (i.e., demic diffusion) or horizontal cultural trans-mission [8]. Genetic evidence suggests that these cultural and technological changes were accompanied by profound genomic transformation, consistent with the migration of people of most likely Anatolian origin [9–12]. In contrast to central Europe, the adoption of agriculture in northern and eastern parts of this conti-nent, in the areas which encompass modern-day Latvia and Ukraine, was slow and relatively recent [13–16]. Although some features of the Neolithic package, such as ceramics, appeared as early as 8,500–7,500 cal BP [17, 18], agriculture was not adopted as a primary subsistence economy until the Late Neolithic/Bronze Age [13–16, 19].

The Neolithic transition in the Baltic and Ukraine thus had a different tempo to that of central Europe, and it is unclear how this may have shaped the genetic composition of these regions. To investigate this, we sampled three Mesolithic and three Neolithic individuals from the archaeological site of Zvejnieki (Latvia), which is one of the richest Stone Age cemeteries in Northern Europe for number of inhumations, as well as duration of use [20, 21] (see theSupplemental Experimental Procedures

for site details). We also sampled a Mesolithic and a Neolithic individual from cemeteries found along the Dnieper River in Ukraine (Vasilyevka 3 and Vovnigi 2, respectively). DNA was ex-tracted from the petrous portion of the temporal bone (see the

Experimental Procedures), which yielded between 4.30% and 55.99% endogenous DNA for all samples. Samples were shotgun sequenced using Illumina sequencing technology to between 0.22- and 4.37-fold coverage (Figure 1). The authen-ticity of the data was assessed in silico by examining the data for signatures of post-mortem DNA damage and evaluating the mitochondrial contamination rate in all samples along with the X chromosome contamination rate in males (see the

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Supplemental Experimental Procedures). All samples had degradation patterns typical of ancient DNA (Figure S1) and low contamination estimates of1% or less (Table 1).

Episodes of Continuity and Change during the Mesolithic and Neolithic in the Baltic

The two earliest samples in our Baltic time series, Latvia_HG1 (8,417–8,199 cal BP), associated with the Kunda culture, and Latvia_HG2 (7,791–7,586 cal BP), associated with the Narva culture, derive from the Late Mesolithic period [17, 21]. A third sample, Latvia_HG3 (7,252–6,802 cal BP), dates to the Late Mesolithic/Early Neolithic period, with the burial showing no ma-jor departures from the preceding Mesolithic traditions [21]. Prin-cipal component analysis (PCA) with ancient samples projected onto modern Eurasian genetic variation (see theSupplemental Experimental Procedures) shows that these three hunter-gath-erer samples group together in a PCA plot (first two components,

Figures 2A andS1A). In keeping with their geographical origins, they are in an intermediate position between Western European hunter-gatherer samples (WHG; from Luxembourg, Hungary, Italy, France, and Switzerland) and Eastern European hunter-gatherer samples (EHG; from Russia). They are composed of the same (blue) major component as these other hunter-gatherer groups in an ancestry coefficient decomposition analysis per-formed using ADMIXTURE [25] (Figure 2B), suggesting a close relationship between these groups. We found that although the Latvian Mesolithic samples share closer affinity to WHG than to EHG, the Latvian Mesolithic samples do not belong entirely to either hunter-gatherer group (tested usingDstatistics [27], which offer a formal test of admixture;Table 2). This suggests that they may be a previously unsampled component of a

hunt-er-gatherer meta-population that stretched across Northern Eu-rope during the early Holocene.

[image:3.603.54.546.99.347.2]

Next we sampled two Middle Neolithic individuals, Lat-via_MN1 (6,201–5,926 cal BP), from an isolated grave located among burials from earlier periods, and Latvia_MN2 (6,179–5,750 cal BP), who was interred in a collective burial with five other individuals. During the Middle Neolithic at Zvejnieki, mortuary practices from the preceding periods were partially maintained, but some new features appeared, including collective burials and votive deposits, which are associated with the Comb Ware culture or its influences in the Baltic [21]. Despite having been roughly contemporaneous, these Middle Neolithic samples cluster in different regions of our PCA plot (Figure 2A) and have distinct profiles in ADMIXTURE analysis (Figure 2B). In both analyses, Latvia_MN1 groups with the Mesolithic Latvian samples, suggesting a degree of continuity across the Meso-lithic-Neolithic transition in this region and consistent with sug-gestions that the eastern Baltic was a genetic refugium for hunter-gatherer populations during the Neolithic period [28]. The persistence of hunter-gatherer ancestry in the Baltic until at least the Middle Neolithic also provides a possible source for the resurgence of hunter-gatherer ancestry that is proposed to have occurred in central Europe from 7,000–5,000 cal BP [1]. In contrast, Latvia_MN2 is placed toward EHG in PCA space and has several components in ADMIXTURE analysis that are found in Native Americans, Siberians, and hunter-gatherer samples from the Caucasus. In keeping with these results, we found that there has been a northern Eurasian influence in the Baltic re-gion since the Mesolithic period, as suggested by significantly positive statistics for the test D(Mbuti, X; Latvia Mesolithic, Latvia_MN2) whenXwas an EHG, modern and ancient Siberian

Figure 1. Geographic Location and Chronologies for Latvian and Ukrainian Sites

Radiocarbon dates (in cal BP) are shown under the sample name. Mean genome coverage is shown in yellow squares, mitochondrial haplogroups in blue squares, and Y chromosome haplogroups for male samples (where discernible) in magenta squares. The chronology of the Latvian site of Zvejnieki is adapted from [21]. The Ukrainian chronology is taken from [18, 22, 23].

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(including the Upper Palaeolithic Mal’ta genome [29]), or Native American (Table 2). This influence is supported archaeologically by the appearance of copper rings and amber jewelry in Middle Neolithic collective burials that bear similarities to artifacts found in Estonia, Finland, and northwestern Russia [21, 30].

The latest Neolithic sample in our Baltic time series, Latvia_LN1 (5,039–4,626 cal BP), which was found in a crouched burial of the type associated with the Late Neolithic Corded Ware culture [21], falls near other Late Neolithic and Bronze Age European and Steppe samples in PCA analysis (Figure 2A). In ADMIXTURE analysis, it is composed of the blue component (Figure 2B), which is predominant in all of the older Latvian sam-ples, but also a green component, which is maximized in hunter-gatherer samples from the Caucasus. A Caucasus-related influence in this sample is also suggested by positive results (although without formal significance, Z > 2) for tests of the form D(Mbuti, Caucasus hunter-gatherer; Latvian Mesolithic, Latvia_LN1). Ancestry related to hunter-gatherers from the Cau-casus has previously been postulated to have arrived in Europe through herders from the Pontic Steppe [1, 31], and these migra-tions could potentially be the source of this ancestry in our sample. Interestingly, this individual lived around the time of later date estimates (4,500–7,000 cal BP) proposed for the split of Proto-Balto-Slavic from other Indo-European languages [3, 4]. There are two major theories to explain the distribution of Indo-European languages that constitute the most widely spoken lan-guage family in the world: (1) they have an Anatolian origin and were spread by Neolithic agriculturalists [32, 33] and (2) they developed in the Pontic Steppe and proliferated through Late Neolithic/Bronze Age migrations [1, 3, 34]. The presence of a Steppe-related component in Latvia_LN1 in the absence of an Anatolian farmer-related genetic input supports a Steppe rather than an Anatolian origin for the Balto-Slavic branch of the Indo-European language family.

It is striking that we did not find evidence for early European or Anatolian farmer admixture in any of our Latvian Neolithic samples using bothDstatistics (Table 2) and ADMIXTURE (

Fig-ure 2A). This lack of admixture is also supported by the mitochondrial haplogroup of the Latvian Neolithic samples (all belong to U;Figure 1), which is prevalent in European hunter-gatherers [1, 35], including our Latvian Mesolithic samples, but not in early farmers. It is interesting that among the grave goods found in the burial of Latvia_LN1 was a chisel made from the bone of a domesticated goat or sheep [17, 21]. The presence of this tool made from a domesticate as well as dietary isotope data (d15N andd13C), which show greater reliance on terrestrial resources than in previous periods [17], is consistent with either the adoption of farming without early European farmer-related genetic admixture or the existence of trade networks with farming communities that were largely independent of genomic exchange. Although we find no genetic input from Anatolian or early European farmers in our time series, ADMIXTURE analysis of an Estonian Corded Ware sample [26] (Figure 2B) has sug-gested that this farmer genetic influence, which is present in contemporary Northern European populations (Figure S2), had arrived in the Baltic by at least the Bronze Age.

The Neolithic Transition in Ukraine

[image:4.603.59.551.115.265.2]

The Ukrainian Mesolithic and Neolithic male samples (Ukraine_HG1 [11,143–10,591 cal BP] and Ukraine_N1 [6,469– 6,293 cal BP], respectively) cluster tightly together between WHG and EHG samples in PCA analysis (Figure 2A). They form a clade with respect to other modern and ancient sam-ples when tested using genome-wideDstatistics (D(Mbuti,X; Ukraine_HG1, Ukraine_N1); Table S1), and their mitochondria belong to the U haplogroup, which has been found in80% of European hunter-gatherer samples [1, 35]. These results suggest a degree of continuity across 4,000 years from the Mesolithic to the Neolithic period in the Dnieper Rapids. In ADMIXTURE analysis (Figure 2B), both Ukrainian samples are composed almost entirely of the European hunter-gatherer (blue) component, with a smaller green component that is also found in EHG. This green component is slightly larger in the Neolithic sample than in the Mesolithic sample, which is

Table 1. Alignment and Contamination Results for Latvian and Ukrainian Ancient Samples

Sample Site Context Burial Aligned Reads

Aligned Reads (%)

MT Coverage

MT Contamination (c+md/c md)

X Contamination (Test 1/Test 2) Latvia_HG1 Zvejnieki Mesolithic; Kunda culture 313 54,784,565 49.26 47.83 0.68/0.04

Latvia_HG2 Zvejnieki Mesolithic; Narva culture 93 172,707,718 55.99 114.97 0.94/0.19 0.92 ± 0.08/0.88 ± 0.17 Latvia_HG3 Zvejnieki Mesolithic/Early Neolithic 121 37,749,963 45.51 40.29 0.77/0.10 0.99 ± 0.26/0.72 ± 0.37 Latvia_MN1 Zvejnieki Middle Neolithic 124 6,648,453 5.22 8.14 0.97/0.50

Latvia_MN2 Zvejnieki Middle Neolithic; Comb Ware culture

221 59,800,396 37.51 48.54 0.69/0.10 Latvia_LN1 Zvejnieki Late Neolithic; Corded Ware

culture

137 9,222,060 7.48 9.58 1.09/0.00 Ukraine_HG1 Vasilyevka Mesolithic 37 9,528,908 4.30 5.49 0.29/0.29 Ukraine_N1 Vovnigi Neolithic; Dnieper-Donets

culture

2 10,741,415 12.04 6.06 1.06 0.28

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in keeping withDstatistics that suggest increased affinity with ancient northern Eurasians from the Mesolithic to the Neolithic in Ukraine (Table S1). It is intriguing that we find an increased affinity to northern Eurasian samples in both Ukraine and Latvia during the Neolithic period. This could be the result of increased connectivity in Europe at this time. More extensive sampling will reveal whether this is a feature of the Neolithic across Northern and Eastern Europe.

Relationship of Ancient Samples to Modern Populations The ancient Latvian and Ukrainian samples fall close to modern Northern and Eastern European populations in PCA analysis ( Fig-ures 2A andS1A), suggesting a degree of continuity in both re-gions since the Mesolithic period. Outgroupf3statistics, which

measure shared genetic drift between populations, further sup-port this as they show that these ancient samples share most af-finity with modern populations from Northern and Eastern Europe (Figure S3). Further, the Y chromosomes of two of our Latvian Mesolithic samples were assigned to haplogroup R1b (the maximum-likelihood sub-haplogroup is R1b1b), which is the

most common haplogroup found in modern Western Europeans [36]. This haplogroup has been found at low frequencies before the Late Neolithic in Western Europe [1, 35] but at higher fre-quencies in Russia and is suggested to have spread into Europe from the East after 5,000 cal BP [1]. The presence of this hap-logroup in Mesolithic Latvia points to a more westward ancestral range. We found that the three Mesolithic Latvian samples are predicted to have had the derived variant (rs12913832) of the

HERC2gene associated with blue eye color (Figure S3B andTable

S2). Blue eye color is found at high frequencies in Northern Europe today, and these results suggest that this phenotype was already present in the Baltic by the Mesolithic period. We also found tenta-tive evidence for progressive skin depigmentation in Latvia based on mutations in theSLC24A5andSLC45A2genes (rs1426654 and rs16891982, respectively;Figure S3B andTable S2).

DISCUSSION

The Neolithic transitions in the Baltic and Dnieper Rapids region of Ukraine show very different archaeological and genetic

[image:5.603.86.509.100.401.2]

A B

Figure 2. PCA and ADMIXTURE Analysis for Ancient Latvian and Ukrainian Samples

(A) Ancient data presented in this study as well as published ancient data (seeData S1for sample details) were projected onto the first two principal components defined by selected modern Eurasians from the Human Origins dataset (see theSupplemental Experimental Procedures). Our Latvian Mesolithic samples cluster tightly together between western and eastern hunter-gatherers in PCA space, whereas the Latvian Neolithic samples are more variable in their position, sug-gesting impacts from exogenous populations. The Ukrainian Mesolithic and Neolithic samples fall close together between western and eastern hunter-gatherers, suggesting a degree of continuity across the Mesolithic-Neolithic boundary in this region.

(B) ADMIXTURE ancestry components (K= 17) [25] for ancient samples showing that the Latvian Neolithic samples do not have the yellow component that dominates in Anatolian and early European farmers. The Latvian and Ukrainian samples presented in this study are displayed in a gray box and at twice the height of the other ancient samples for ease of visualization. The arrow shows an Estonian Bronze Age sample (RISE00) [26] that has a yellow component, suggesting that an early European farmer genetic influence had arrived in the Baltic by the Bronze Age.

HG, hunter-gatherer; BA, Bronze Age; W, western; C, Central. See alsoFigures S1–S4.

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dynamics to those observed in Central and Western Europe. Although in central Europe pottery and agriculture arrive as a package, in the Baltic and Dnieper Rapids the onset of the Neolithic is characterized by the appearance of ceramics, with a definitive shift to an agro-pastoralist economy only occurring during the Late Neolithic/Bronze Age [13–16, 19]. Although the prolonged and piecemeal uptake of Neolithic characteristics in

[image:6.603.61.550.192.737.2]

these regions makes it challenging to attribute a definitive shift in ideology or lifestyle, it does, along with evidence for continu-ities in material culture and settlement patterns, suggest that Neolithic features were predominantly adopted by indigenous hunter-gatherers in this region [13–16, 37]. We find genetic evi-dence in support of this in the affinity of the Latvian and Ukrainian Neolithic samples, Latvian_MN1 and Ukrainian_N1, to earlier

Table 2. KeyDStatistics of the FormD(A,B;X,Y) for Latvian Samples

A B X Y D Z Score Loci

Latvian Mesolithic Samplesa

Mbuti Latvia_HG EHG WHG 0.0787 13.064 103,420 Mbuti EHG Latvia_HG WHG 0.0281 4.797 103,420 Mbuti WHG Latvia_HG EHG 0.1065 17.418 103,420

Mbuti Latvia_HG Karelia (EHG) Bichon (WHG) 0.0801 11.725 3,188,010

Mbuti Latvia_HG Karelia (EHG) Loschbour (WHG) 0.0928 13.521 3,204,237

Mbuti Karelia (EHG) Latvia_HG Bichon (WHG) 0.0432 6.494 3,188,010

Mbuti Karelia (EHG) Latvia_HG Loschbour (WHG) 0.0354 5.367 3,204,237

Mbuti Bichon (WHG) Karelia (EHG) Latvia_HG 0.1228 17.680 3,188,010

Mbuti Loschbour (WHG) Karelia (EHG) Latvia_HG 0.1277 18.643 3,204,237

Latvia_MN1b

Mbuti_AF Iran_LN Latvia_HG Latvia_MN1 0.0427 1.459 7,261 Mbuti_AF Anatolia_ChL Latvia_HG Latvia_MN1 0.0249 0.907 8,289 Mbuti_AF Kennewick Latvia_HG Latvia_MN1 0.0181 0.685 9,026 Latvia_MN2c

Mbuti Zapotec Latvia_HG Latvia_MN2 0.0295 4.171 74,461 Mbuti Guarani Latvia_HG Latvia_MN2 0.0303 4.027 74,461 Mbuti Aymara Latvia_HG Latvia_MN2 0.0282 3.926 74,461 Mbuti EHG Latvia_HG Latvia_MN2 0.0346 3.734 70,000 Mbuti AfontovaGora3 Latvia_HG Latvia_MN2 0.0658 3.519 19,541 Mbuti MA1 Latvia_HG Latvia_MN2 0.0381 3.441 53,389

Mbuti Karelia (EHG) Latvia_HG Latvia_MN2 0.0386 5.742 2,165,498

Mbuti MA1 Latvia_HG Latvia_MN2 0.0553 7.355 1,799,638

Mbuti Karitiana Latvia_HG Latvia_MN2 0.0366 5.307 2,693,045

Latvia_LN1d

Mbuti CHG Latvia_HG Latvia_LN1 0.0312 2.081 20,994 Mbuti Iran_N Latvia_HG Latvia_LN1 0.0275 1.483 16,000 Mbuti Iran_ChL Latvia_HG Latvia_LN1 0.0203 1.457 19,027 Mbuti Iran_LN Latvia_HG Latvia_LN1 0.0319 1.320 9,481 Mbuti Iranian_Jew_WA Latvia_HG Latvia_LN1 0.0106 1.091 20,998

Mbuti Kotias (CHG) Latvia_HG Latvia_LN1 0.0182 2.138 715,061

Latvian Neolithic Samplese

Mbuti Anatolia_N Latvia_HG Latvia_MN1 0.0013 0.108 16,255 Mbuti Europe_EN Latvia_HG Latvia_MN1 0.0055 0.476 16,272 Mbuti Anatolia_N Latvia_HG Latvia_MN2 0.0246 3.607 74,355 Mbuti Europe_EN Latvia_HG Latvia_MN2 0.0335 5.055 74,460 Mbuti Anatolia_N Latvia_HG Latvia_LN1 0.0221 2.136 20,969 Mbuti Europe_EN Latvia_HG Latvia_LN1 0.0308 2.952 20,998

Mbuti Stuttgart Latvia_HG Latvia_MN1 0.0168 1.804 581,303

Mbuti NE1 Latvia_HG Latvia_MN1 0.0161 1.704 581,758

Mbuti Stuttgart Latvia_HG Latvia_MN2 0.0300 4.527 2,722,280

Mbuti NE1 Latvia_HG Latvia_MN2 0.0272 3.871 2,724,548

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Mesolithic samples from the same respective regions. However, we also find indications of genetic impact from exogenous pop-ulations during the Neolithic, most likely from northern Eurasia and the Pontic Steppe. These influences are distinct from the Anatolian-farmer-related gene flow found in central Europe dur-ing this period. It is interestdur-ing to note that even in outlydur-ing areas of Europe, such as Sweden and Ireland [38, 39], an Anatolian-farmer-related genetic signature is present by the Middle to Late Neolithic period (5,300–4,700 cal BP). We conclude that the gradual appearance of features associated with the Neolithic package in the Baltic and Dnieper Rapids was not tied to the same major genetic changes as in other regions of Europe. The emergence of Neolithic features in the absence of immigra-tion by Anatolian farmers highlights the roles of horizontal cul-tural transmission and potentially independent innovation during the Neolithic transition.

EXPERIMENTAL PROCEDURES

DNA was extracted from a petrous bone of our samples in dedicated ancient DNA facilities (see theSupplemental Experimental Procedures). Libraries were prepared and sequenced using 50–100 bp Illumina single-end sequencing, and reads were aligned to the GRCh37 build of the human genome with the mitochondrial sequence replaced by the revised Cambridge reference sequence. The authenticity of the data was assessed by looking for short average sequence length and patterns of molecular damage and estimating the mitochondrial and X chromosome contamination rates (see the Supple-mental ExperiSupple-mental Procedures). Sex was determined by examining the ratio of Y chromosome reads to reads aligning to both sex chromosomes [40]. Pseudo-diploid genotypes were called in our sample at positions that overlap-ped autosomal genotypes in the Human Origins dataset (110,507 positions) and merged with publicly available ancient genotypes (see theSupplemental Experimental Procedures). The relationship between our ancient samples and other modern and ancient populations was assessed using PCA, ADMIXTURE,Dstatistics, andf3statistics (see theSupplemental Experimental

Procedures). Mitochondrial and Y chromosome haplogroups were determined using HAPLOFIND and Yfitter, respectively. Genotypes associated with particular phenotypes were examined using observed and imputed geno-types as in [2] (see theSupplemental Experimental Procedures,Figure S3, andTable S2).

ACCESSION NUMBERS

The accession number for the sequence data reported in this paper is Euro-pean Nucleotide Archive (ENA): PRJEB18067.

SUPPLEMENTAL INFORMATION

Supplemental Information includes Supplemental Experimental Procedures, four figures, two tables, and one data file and can be found with this article on-line athttp://dx.doi.org/10.1016/j.cub.2016.12.060.

AUTHOR CONTRIBUTIONS

D.G.B., R.P., and A.M. supervised the study. E.R.J., D.G.B., and A.M. analyzed genetic data. R.P., G.Z., V.M., and P.R.N. provided samples and/or input about archaeological context. E.L. helped interpret isotope analyses. E.R.J., A.M., P.R.N., and D.G.B. wrote the manuscript with input from all co-authors.

ACKNOWLEDGMENTS

This research was supported by a European Research Council (ERC) Starting Grant (ERC-2010-StG 263441) and Irish Research Council Advanced Research Project Grant to R.P. D.G.B. and A.M. were also supported by the ERC (295729-CodeX and 647787-LocalAdaptation, respectively). P.R.N. was supported by a FP7MC Career Integration Grant (NEMO-ADAP; no. 322261). We would like to thank Veronika Siska, Cristina Gamba, Rui Marti-niano, Russell McLaughlin, Lara Cassidy, and Olesia Kononenko for their support.

Received: October 30, 2016 Revised: November 10, 2016 Accepted: December 29, 2016 Published: February 2, 2017

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2.Gamba, C., Jones, E.R., Teasdale, M.D., McLaughlin, R.L., Gonzalez-Fortes, G., Mattiangeli, V., Domboro´czki, L., K}ova´ri, I., Pap, I., Anders, A., et al. (2014). Genome flux and stasis in a five millennium transect of European prehistory. Nat. Commun.5, 5257.

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Table 2. Continued

A B X Y D Z Score Loci

Mbuti Stuttgart Latvia_HG Latvia_LN1 0.0246 2.955 715,090

Mbuti NE1 Latvia_HG Latvia_LN1 0.0215 2.373 715618

Latvia_HG, Latvian hunter-gatherers; WHG, western hunter-gatherers; EHG, eastern hunter-gatherers; Iran_LN, Iranian Late Neolithic; Anatolia_ChL, Anatolian Chalcolithic; CHG, Caucasus hunter-gatherers; Iran_N, Iranian Neolithic; Iran_ChL, Iranian Chalcolithic; Anatolian_N, Anatolian Neolithic; Europe_EN, European Early Neolithic. Tests performed using the whole genome panel are italicized; otherwise, tests were performed using the Human Origin transversion SNP panel. Ancient samples are shown in bold. Samples include in each ancient group can be found inData S1. SeeTable S1for keyDstatistics for Ukrainian samples.

aThe Latvian Mesolithic samples share more affinity to WHG than to EHG, but they do not belong entirely to either group. bThere is no evidence for admixture in our Latvian Neolithic sample, Latvia_MN1 (the three largest positive statistics are shown).

cThere is an eastern influence in the Latvian Middle Neolithic sample, Latvia_MN2, as compared to the Latvian Mesolithic samples (the three most significantly positive results with ancient and modern populations/individuals from the Human Origins SNP panel dataset are shown).

dLargest positive results for the testD(Mbuti,X; Latvia_HG, Latvia_LN1). ADMIXTURE results suggest that there may have been a CHG-related influence in Latvia during the Late Neolithic period; however, althoughDstatistics to test this are positive, they do not reach significance.

eWe do not find evidence for early European/Anatolian farmer admixture in our Latvian Neolithic samples.

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Figure

Figure 1. Geographic Location and Chronologies for Latvian and Ukrainian SitesRadiocarbon dates (in cal BP) are shown under the sample name
Table 1. Alignment and Contamination Results for Latvian and Ukrainian Ancient Samples
Figure 2. PCA and ADMIXTURE Analysis for Ancient Latvian and Ukrainian Samples
Table 2. Key D Statistics of the Form D(A,B; X,Y) for Latvian Samples
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